Control of Alameda’s ferries could be wrenched away from the city under a bill approved by the California State Senate in the early morning hours Wednesday.

Under Senate Bill 976, Alameda and Vallejo ferry services would be consolidated and placed under the authority of one newly created body to better coordinate emergency response and provide more efficient service.

City officials are not sure how the move will affect Alameda, which runs the Alameda/Oakland Ferry Service and the Harbor Bay Ferry service.

“There’s a lot of issues that need to be resolved, a lot of vague language about what it means to consolidate ferry services,” said Alameda Deputy City Manager Lisa Goldman. “We’re looking into that. We’re looking to work with the author of the bill and others … (including) our own senator, (Don Perata), … to try to understand the intent and what the language means.”

Goldman added, “I understand they will do some clarification language, what they call ‘cleanup’ language, next year.”

Under the bill, the Water Transit Authority, which was created to run new ferry services in South San Francisco and other locations, would cease to exist. It would be replaced by a new organization, the Bay Area Water Emergency Transportation Authority.

The 11-member board that now oversees the Water Transit Authority — which includes Alameda Mayor Beverly Johnson — would be replaced with a five-member board chosen by the governor, the Senate and the Assembly.

The possibility of Alameda not having a representative on the board also concerns the city, Goldman said.

“We understand the important role ferries can play in a disaster situation,” she said, “and we’re very supportive of ferries being a part of a regional response to emergencies. But we want to ensure our services don’t suffer and residents enjoy the good ferry service they now enjoy.”

Shirley Douglas, the community relations manager with the Water Transit Authority, said the board had concerns about its make-up, but otherwise was still digesting the plan. The authority board was scheduled to meet today to talk about it, she said.

“We knew there was some legislation being discussed,” she said, “but the specifics of it was a surprise to us.”

The Senate approved the bill Wednesday morning by a 23-14 vote. Late Tuesday night, it sailed through the Assembly largely along party lines.

Gov. Arnold Schwarzenegger has until Oct. 14 to sign the bill. If it passes, the state would have until July 1, 2009, to create and implement a new ferry management plan.

“We have set it up that nothing is going to happen until a yearlong public transition plan is made,” said Alicia Trost, the press secretary for Perata, who is one of the key supporters of the bill.

“There is a clear need to have a disaster response and recovery system in case of a major disaster,” Trost added.

The sponsor of the bill, state Sen. Tom Torlakson, D-Antioch, and his staff, could not be reached for comment Wednesday.

John Grubb, vice president of communications for a business-based advocacy group called the Bay Area Council, took credit for raising the issue with state lawmakers.

He said despite the surprise some have expressed over the law, it has been two years in the making.

He said the new law would set up an emergency ferry organization with a funding stream from voter-approved bridge toll increases, to the tune of $250 million.

That would provide for new boats, new terminals and “perhaps feeder buses as well,” he said.

“How this will affect residents of Oakland and Alameda is they will have more options on ferry boats that will likely be more efficient, with more choices of where to go,” he said. “And in the event of an earthquake, a much higher chance of survival and recovery.”

Following a major earthquake, the boats not only would provide ways to get around, Grubb said, but would also provide an important vessel for transporting needed supplies.